Let us stipulate that Israel's blockade of Gaza—which has been policy since 2007, when Hamas took control after winning the parliamentary elections yet kept up mortar attacks against Israeli territory—is legitimate. (It's worth noting, in this context, that Egypt has been enforcing a blockade on land, as well.)

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It is also certainly clear, by their own admission, that the organizers of the six-ship flotilla sailing toward Gaza intended not merely to deliver aid to Palestinians but also to challenge the blockade, a move that they had to expect might provoke a confrontation.

That being the case, Israeli commanders had the right—as a matter of national security—to block the ship's passage, even by boarding it if necessary, especially if they first issued radio warnings to turn back or face consequences (as, in this instance, they did).

However, as Clausewitz famously noted, war is politics by other means. A blockade is an act of war (in this case, an extension of the fact that Hamas considers itself to be at war with Israel); when it comes to wars involving Israel, any act of violence is fraught with politics in every meaning of the word. And in this sense, Israel's actions on the Mavi Marmara reflect a total disconnect between military means and political ends.

Navies have been mounting blockades for centuries; it's one of the things that navies were created to do. The Israeli navy has been turning back the occasional boatload of peace activists or Palestinian protesters ever since the Gaza blockade went into effect, with so little tumult the incidents have hardly been noticed.

Usually, the boats have been turned back or towed to Ashdod, an Israeli harbor north of Gaza, where the aid parcels are inspected—and, in some cases, confiscated—before being sent on to Gaza by truck. On at least four occasions, though, boats have been allowed to land in Gaza's harbor, with no noticeable compromise to Israeli security.

True, Sunday's flotilla was by far the largest: six boats, one quite large, carrying a total of 600 people and reportedly 10,000 tons of aid. Still, these were registered civilian vessels, hoisting the Turkish flag and—at the time of the incident—sailing in international waters.

Israel says the commandos fired only in self-defense. It has been reported that the activists went at the commandos with clubs, chairs, steel pipes, fists, and the occasional knife—no doubt frightening, especially if the Israeli landing crew didn't expect resistance. But this was an elite Israeli team, presumably trained to deal with organized military foes armed with grenades, machine guns, and worse.

The questions here are fairly obvious: Why shouldn't the Israeli commandos have expected resistance, at least as an operational premise? Why weren't they equipped with nonlethal weapons? Why didn't they fire a few canisters of tear gas as they boarded or once the first brickbats flew?

There was nothing surprising, after all, about the appearance of these boats. They had converged and set sail from Cyprus a day earlier. More to the point, the activists had been planning their voyage—and very publicly announcing their intentions—for weeks.

The Israelis, in short, had plenty of time to issue warnings, explain to the public (including to the Turkish government) what steps might ensue if the activists carried out their plans—and, more important, to plan what the Israeli navy should do if the boats broke through the 28-kilometer "exclusion zone" (which apparently they didn't quite cross before the landing took place in any case).

That the Israeli government did nothing to gain the upper hand in the all-but-certain propaganda battle to come is baffling.

But what's appalling—really mind-twisting—is that the Israelis seem to have had no plan for what to do under such circumstances in general.

Again, a blockade is a military act; this blockade has been in effect, and has had to be enforced several times, for three years. At least once before, in June 2009, Israeli commandos boarded a boat carrying aid for Hamas and towed it to Ashdod without incident. Other nations' navies, as well as multinational task forces, have boarded boats suspected of carrying drugs, nuclear materials, or other contraband for many years. There are time-tested, well-rehearsed methods for doing this without triggering violence—and for quickly suppressing violence, should it break out.

Yet the Israeli navy seems to have had no plan of what to do if commandos boarded a boat and its personnel fought back, whether with fists, bricks, guns, or whatever. Could this be? Or if there were plans, if the commandos have held training exercises under every conceivable scenario, why did everything go wrong here?

More broadly, doesn't the Israeli navy have plans, hasn't it conducted exercises—just as navies worldwide have plans and have conducted exercises—to block these sorts of incursions without storming the boat to begin with? This wasn't an aircraft carrier or a destroyer heading toward Gaza's harbor; there are ways to disable boats of this size without sinking them. There are also ways to block a boat from reaching a coastline without intercepting it in international waters.

When Israeli lawmakers and opinion leaders—not just the typical critics of Israel, but Israelis themselves—call for an investigation of what happened, this is the ultimate question they're getting at: Are Israel's political and military leaders carefully, intelligently, competently defending Israeli security?

The failure onboard the Mavi Marmara was not merely a matter of technical details or tactical mistakes; it was—or at least appears to have been—the result of gross incompetence and strategic malfeasance.

Any Israeli Cabinet minister or military commander of even the slightest intelligence must know that military actions, especially military actions against civilians—even when justified—have political consequences. This doesn't mean actions shouldn't be taken—just that calculating their costs and benefits should, by this time, be second nature.

It is in this context that Ha'aretz columnist Ari Shavit wrote today that, in its actions onboard the Mavi Marmara, "Israel is serving Hamas' interests better than Hamas itself has ever done."

Here is how Hamas' interests have been served so far:

Under severe pressure, Egypt, which has blockaded Gaza by land for its own political reasons, has opened its borders (at least for now), a move that is likely to facilitate more weapons shipments than the most extreme estimates of potential smuggling from the Mavi Marmara would have supplied.

Turkey, the only predominantly Muslim country that regards Israel as an ally, has recalled its ambassador from Tel Aviv amid massive anti-Israeli protests in the streets of Istanbul.

Prime Minister Benjamin Netanyahu, who was on his way to Washington to discuss the resumption of Palestinian peace talks with President Barack Obama, had to go home (for obvious reasons), and the prospect for renewed diplomacy—which had gained much support in the region—has, to say the least, diminished.

The case for tighter sanctions against Iran, to the extent that they involve sympathy with Israel's security concerns, has been dealt a setback, just as the U.N. nuclear agency has announced that Iran has enough fuel to build two A-bombs (though the fuel still needs to be enriched).

The U.N. Security Council has condemned Israel's actions, and countless aid groups, including no doubt several that are hostile to Israel, are sailing toward Gaza, as if to dare the Israelis to fire on them too and, in any case, to deal another blow against the legitimacy of the blockade.

In sum, in order to keep one ship from delivering aid directly to Hamas—and, as Ha'aretz put it, choosing "the worst of all possible options" to do so—Israel has plunged itself into the deepest state of isolation that it's experienced in years.

One way to begin extracting itself from this morass might be to reconsider the Gaza blockade. The logic of the policy is unassailable: The ruling party, Hamas, doesn't recognize Israel's right to exist and occasionally hurls mortar shells at Israeli territory. Israel is reasonable to make sure that goods coming in to Gaza don't include weapons.

However, the execution of the policy has been unreasonably draconian. Israeli officials take so long to inspect the cargo that medicines often expire by the time they reach Palestinian patients. Construction materials, such as pipes and heavy metals, are confiscated on the grounds that they could be used to make weapons, and so the Gaza authorities are unable to rebuild destroyed neighborhoods.

According to some estimates, the flow of goods coming into Gaza—not just food and medical supplies but goods of all sorts—amounts to a mere one-quarter of pre-blockade levels.

The situation has not only spawned a humanitarian crisis, it has also played into the hands of militants who seek to exploit the genuine concern of international aid groups for their own advantage—and to further portray Israeli policy as savage while evading their own responsibility for the continued hostilities.

At the very least, Israel's leaders need to rethink what (to some extent, legitimate) goals the blockade serves—and how those goals might be achieved without incurring such dreadful costs.